We investigate a powerful new sensing platform based on upconversion luminescence in NaYF₄: Yb/Er nanocrystals loaded inside a suspended-core microstructured optical fibre. The use of a NIR source enables autofluorescence from the glass to be reduced compared to using visible sources for excitation of fluorescence. We demonstrate a substantial improvement in the detection limit that can be achieved in a suspended-core fibre sensor, with detection limits as low as 660 fM achieved. This is a factor of 15× better than the best results previously reported using Quantum dots in a similar fibre.